Steps to reproduce:

1. Set up a Perforce server. (local will do.)
2. Create a repository and copy the project to the Perforce repo.
3. Check out the project from Perforce.
4. Set up the perforce integration in Unity with the repo and make sure it's connected and working.
5. Close Unity.
6. Make sure the Assets/Resource/Internal-Halo.shader contents are the same as the attached ( note the legacy 'o.pos = mul (UNITY_MATRIX_MVP, v.vertex);' line), and checked into the Perforce repository, and NOT checked out.
7. Make sure the Assets/Resource/TrafficLightHalo.shader contents are the same as the attached and checked into the Perforce repository, and NOT checked out.
8. Also make sure ProjectSettings\GraphicsSettings.asset is the same as attached, checked into Perforce, and NOT checked out.
9. Now open the project in Unity.
10. Unity should modify Internal-Halo.shader, TrafficLightHalo.shader and GraphicsSettings.asset without checking them out from Perforce.
To confirm this, open P4V and see no files in the pending changelist.
Select Reconcile OFffline work, and the files should be visible.

Expected: Files should not be modified without perforce checking them out. Upon launch the modified files should be checked out
Actual: Files get modified, not checked out, Perforce doesn't know there were changes.

Reproduced on: 5.5.4p1, 5.6.1p4, 2017.1.0f2, 2017.2.0b2